Skip to content

index.md

Latest commit

 

History

History
69 lines (52 loc) · 2.84 KB

index.md

File metadata and controls

69 lines (52 loc) · 2.84 KB
Raw

Advanced Documentation

This directory contains detailed documentation for ln2t_tools developers and advanced users.

Quick Navigation

Document Purpose Audience Time
Data Import Guide BIDS conversion for all data types Lab administrators, data managers 30-45 min
Adding a New Tool Extend ln2t_tools with new pipelines Tool developers, contributors 45-60 min
Instance Management Control parallel processing limits Administrators 5-10 min
MELD Graph Setup Advanced FCD lesion detection workflow Researchers using MELD 20-30 min

Documentation by Topic

Data Management

Data Import Guide

Comprehensive guide to converting raw neuroimaging data to BIDS format. Covers:

  • DICOM: Conversion with dcm2bids and optional defacing
  • MRS: Magnetic Resonance Spectroscopy conversion with spec2nii
  • Physiological Data: GE monitor data processing with phys2bids
  • MEG: Complete MEG workflow including MaxFilter derivatives, calibration files, and head shape extraction
  • Configuration file setup for each datatype
  • Directory structure and naming conventions
  • Participants mapping and session handling

Use when: Setting up data import pipelines for your lab

Tool Development

Adding a New Tool

Step-by-step guide to developing and integrating new neuroimaging tools into ln2t_tools. Covers:

  • Tool architecture and BaseTool interface
  • CLI argument handling and validation
  • Container image registration and configuration
  • Creating custom Apptainer container recipes
  • Best practices and advanced features
  • HPC script generation and custom processing workflows

Use when: You want to add a new pipeline to ln2t_tools

Administration

Instance Management

Understanding and controlling parallel job limits. Learn about:

  • Default limits and configuration
  • Lock file system and metadata
  • Automatic cleanup mechanisms
  • Troubleshooting resource issues

Use when: Managing multiple concurrent processing jobs or debugging resource conflicts

MELD Graph Setup

Advanced configuration for MELD Graph lesion detection. Covers:

  • Three-step workflow: Download weights → Harmonization → Prediction
  • Scanner-specific harmonization
  • FreeSurfer integration and precomputed outputs
  • Feature extraction and reuse
  • Demographics configuration
  • Complete example workflows

Use when: Running MELD Graph for focal cortical dysplasia detection

Getting Help

  • Main README: Start with ../README.md for general usage
  • Specific tools: Run ln2t_tools <tool> --help for tool-specific options
  • Issues: Check the project repository for known issues and support